def output_pickle_file(self, results_output_dir, sample_label): print "Serializing a total of %d events by Pickle." %(len(self.events)) pickle_output_dir = os.path.join(results_output_dir, 'pickle') if not os.path.isdir(pickle_output_dir): os.mkdir(pickle_output_dir) pickle_events_filename = os.path.join(pickle_output_dir, sample_label + '.pickle') pickle_utils.write_pickled_file(self.events, pickle_events_filename) return pickle_events_filename
def output_pickle_file(self, results_output_dir, sample_label):
print "Serializing a total of %d events by Pickle." % (len(
self.events))
pickle_output_dir = os.path.join(results_output_dir, 'pickle')
if not os.path.isdir(pickle_output_dir):
os.mkdir(pickle_output_dir)
pickle_events_filename = os.path.join(pickle_output_dir,
sample_label + '.pickle')
pickle_utils.write_pickled_file(self.events, pickle_events_filename)
return pickle_events_filename
def serialize_genes(gff_genes, output_dir):
"""
Output genes into pickle files by chromosome, by gene.
"""
genes_by_chrom = defaultdict(dict)
# Split up genes by chromosome
for gene_id, gene_info in gff_genes.iteritems():
gene_obj = gene_info["gene_object"]
gene_hierarchy = gene_info["hierarchy"]
genes_by_chrom[gene_obj.chrom][gene_id] = {
'gene_object': gene_obj,
'hierarchy': gene_hierarchy
}
# Mapping from gene IDs to pickled filename
gene_id_to_filename = {}
# Serialize all the genes in each chromosome into their
# own directory
for chrom, chrom_genes in genes_by_chrom.iteritems():
if chrom.startswith("chr"):
chrom_dir_name = chrom
else:
chrom_dir_name = "chr%s" % (str(chrom))
# Make directory for chromosome if it doesn't already exist
chrom_dir = os.path.join(output_dir, chrom_dir_name)
if not os.path.isdir(chrom_dir):
print "Making directory: %s" % (chrom_dir)
os.makedirs(chrom_dir)
t1 = time.time()
# Serialize each gene into a separate file
num_genes = len(genes_by_chrom[chrom])
for gene_id, gene_info in genes_by_chrom[chrom].iteritems():
gene_filename = os.path.abspath(
os.path.join(chrom_dir, "%s.pickle" % (gene_id)))
pickle_utils.write_pickled_file(
{gene_id: genes_by_chrom[chrom][gene_id]}, gene_filename)
# Record what filename was associated with this gene ID
gene_id_to_filename[gene_id] = gene_filename
t2 = time.time()
print " - Chromosome serialization took %.2f seconds" % (t2 - t1)
# Shelve the mapping from gene ids to filenames
shelved_filename = os.path.join(output_dir, "genes_to_filenames.shelve")
shelved_data = shelve.open(shelved_filename)
for k, v in gene_id_to_filename.iteritems():
shelved_data[k] = v
shelved_data.close()
def serialize_genes(gff_genes, output_dir):
"""
Output genes into pickle files by chromosome, by gene.
"""
genes_by_chrom = defaultdict(dict)
# Split up genes by chromosome
for gene_id, gene_info in gff_genes.iteritems():
gene_obj = gene_info["gene_object"]
gene_hierarchy = gene_info["hierarchy"]
genes_by_chrom[gene_obj.chrom][gene_id] = {"gene_object": gene_obj, "hierarchy": gene_hierarchy}
# Mapping from gene IDs to pickled filename
gene_id_to_filename = {}
# Serialize all the genes in each chromosome into their
# own directory
for chrom, chrom_genes in genes_by_chrom.iteritems():
if chrom.startswith("chr"):
chrom_dir_name = chrom
else:
chrom_dir_name = "chr%s" % (str(chrom))
# Make directory for chromosome if it doesn't already exist
chrom_dir = os.path.join(output_dir, chrom_dir_name)
if not os.path.isdir(chrom_dir):
print "Making directory: %s" % (chrom_dir)
os.makedirs(chrom_dir)
t1 = time.time()
# Serialize each gene into a separate file
num_genes = len(genes_by_chrom[chrom])
for gene_id, gene_info in genes_by_chrom[chrom].iteritems():
gene_filename = os.path.abspath(os.path.join(chrom_dir, "%s.pickle" % (gene_id)))
pickle_utils.write_pickled_file({gene_id: genes_by_chrom[chrom][gene_id]}, gene_filename)
# Record what filename was associated with this gene ID
gene_id_to_filename[gene_id] = gene_filename
t2 = time.time()
print " - Chromosome serialization took %.2f seconds" % (t2 - t1)
# Shelve the mapping from gene ids to filenames
shelved_filename = os.path.join(output_dir, "genes_to_filenames.shelve")
shelved_data = shelve.open(shelved_filename)
for k, v in gene_id_to_filename.iteritems():
shelved_data[k] = v
shelved_data.close()
